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Sample GSM397784 Query DataSets for GSM397784
Status Public on Jul 31, 2010
Title Blood-MND-0574-rep1
Sample type genomic
Source name MND Blood
Organism Homo sapiens
Characteristics study #: Study 2 (Twin)
trio #: NA
twin #: Twin 1
twin info: Monozygotic Concordant for MND
gender: M
phenotype: MND
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was extracted from leukocytes using the phenol chloroform method or Qiamp blood kits (Qiagen Pty Ltd, Doncaster, Vic, Australia), hair using the phenol chloroform method, and from sperm using Pure Sperm 100 kits (Nidacom, Gothenburg, Sweden).
Label biotin
Label protocol According to manufacturer protocol (The Ramaciotti Centre for Gene Function Analysis, Sydney, Australia), Affymetrix dsDNA terminal label.
Hybridization protocol According to manufacturer protocol (The Ramaciotti Centre for Gene Function Analysis, Sydney, Australia)
Scan protocol According to manufacturer protocol (The Ramaciotti Centre for Gene Function Analysis, Sydney, Australia)
Description Affy 6.0 MND Blood
Data processing Data processed using Affymetrix Command Console software and Affymetrix Genotyping Console 3.0.2 software using the Birdseed version 2 algorithm and default settings.
Genotype Call (SNP call): AA, AB, BB, NC, and NoCall; 'Signal' = Summarized signal
Submission date Apr 25, 2009
Last update date Jun 26, 2012
Contact name Roger Pamphlett
Organization name University of Sydney
Street address Blackburn Bld
City University of Sydney
ZIP/Postal code 2006
Country Australia
Platform ID GPL6801
Series (1)
GSE15826 Affymetrix 6.0 study of sporadic motor neuron disease patients and controls.

Data table header descriptions
VALUE Genotype Call (SNP call): AA, AB, BB, NC, and NoCall
CONFIDENCE A value in the range [0,1] with lower values corresponding to greater confidence
FORCED CALL This value is the genotyping call that would be made if the calling algorithm were tuned to the least stringency. Providing this value allows for determining what the calls would have been at a stringency different to that applied to the calls in the second field, without having to re-run the genotyping algorithm
SIGNAL A Summarized signal A
SIGNAL B Summarized signal B

Data table
SNP_A-2131660 AB 0.004941 AB 2487.656982 3119.900391
SNP_A-1967418 AB 0.002357 AB 528.185120 536.692078
SNP_A-1969580 BB 0.002216 BB 1023.473083 3720.401855
SNP_A-4263484 BB 0.003033 BB 495.440247 1924.134277
SNP_A-1978185 AA 0.004595 AA 1690.761230 385.442200
SNP_A-4264431 AA 0.003328 AA 2096.727539 307.207367
SNP_A-1980898 BB 0.000702 BB 235.989426 872.490784
SNP_A-1983139 AA 0.001263 AA 4532.028320 1051.174561
SNP_A-4265735 AA 0.002420 AA 2618.163086 583.054626
SNP_A-1995832 AB 0.001063 AB 2010.855957 1509.380859
SNP_A-1995893 AB 0.004540 AB 1749.244019 2239.218750
SNP_A-1997689 BB 0.005112 BB 912.601135 4086.515137
SNP_A-1997709 AA 0.001002 AA 2440.333008 342.669617
SNP_A-1997896 AA 0.005252 AA 1520.373657 401.128113
SNP_A-1997922 AB 0.003721 AB 853.614136 725.742249
SNP_A-2000230 AA 0.001269 AA 2867.516846 1100.076660
SNP_A-2000332 BB 0.003304 BB 1295.834106 4312.549805
SNP_A-2000337 AA 0.004451 AA 1626.688354 218.535416
SNP_A-2000342 AA 0.000978 AA 4280.935547 1005.961731
SNP_A-4268173 AA 0.001699 AA 1417.215210 291.346283

Total number of rows: 909622

Table truncated, full table size 46139 Kbytes.

Supplementary file Size Download File type/resource
GSM397784.CEL.gz 31.5 Mb (ftp)(http) CEL
GSM397784.chp.gz 13.1 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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